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- PDB-4pl0: Crystal structure of the antibacterial peptide ABC transporter Mc... -

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Basic information

Entry
Database: PDB / ID: 4pl0
TitleCrystal structure of the antibacterial peptide ABC transporter McjD in an outward occluded state
ComponentsMicrocin-J25 export ATP-binding/permease protein McjD
KeywordsTRANSPORT PROTEIN / ABC transporter / membrane protein / occluded
Function / homology
Function and homology information


bacteriocin transport / bacteriocin immunity / ABC-type transporter activity / protein transport / ATP hydrolysis activity / ATP binding / plasma membrane
Similarity search - Function
Type 1 protein exporter / ABC transporter transmembrane region / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. ...Type 1 protein exporter / ABC transporter transmembrane region / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Microcin-J25 export ATP-binding/permease protein McjD
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsChoudhury, H.G. / Beis, K.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Structure of an antibacterial peptide ATP-binding cassette transporter in a novel outward occluded state.
Authors: Choudhury, H.G. / Tong, Z. / Mathavan, I. / Li, Y. / Iwata, S. / Zirah, S. / Rebuffat, S. / van Veen, H.W. / Beis, K.
History
DepositionMay 15, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 18, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 25, 2014Group: Database references
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Microcin-J25 export ATP-binding/permease protein McjD
B: Microcin-J25 export ATP-binding/permease protein McjD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,6398
Polymers130,9652
Non-polymers1,6746
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18270 Å2
ΔGint-105 kcal/mol
Surface area46640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.830, 107.920, 232.960
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Microcin-J25 export ATP-binding/permease protein McjD / Microcin-J25 immunity protein / Microcin-J25 secretion ATP-binding protein McjD


Mass: 65482.418 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: mcjD / Plasmid: pWaldoGFPd / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: Q9X2W0
#2: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Sugar ChemComp-BNG / nonyl beta-D-glucopyranoside / Beta-NONYLGLUCOSIDE / nonyl beta-D-glucoside / nonyl D-glucoside / nonyl glucoside


Type: D-saccharide / Mass: 306.395 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H30O6 / Comment: detergent*YM
IdentifierTypeProgram
b-nonylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.88 Å3/Da / Density % sol: 68.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 5.5
Details: 100 mM sodium citrate pH 5.5, 45 mM NaCl and 26% PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 5, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.7→48.96 Å / Num. obs: 56627 / % possible obs: 99.8 % / Redundancy: 3.7 % / Biso Wilson estimate: 69.33 Å2 / Net I/σ(I): 12.1
Reflection shellResolution: 2.7→2.78 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 1.5 / % possible all: 99.6

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Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ONJ

2onj


Resolution: 2.7→48.96 Å / Cor.coef. Fo:Fc: 0.8628 / Cor.coef. Fo:Fc free: 0.8774 / SU R Cruickshank DPI: 0.454 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.433 / SU Rfree Blow DPI: 0.281 / SU Rfree Cruickshank DPI: 0.289
RfactorNum. reflection% reflectionSelection details
Rfree0.266 2891 5.11 %RANDOM
Rwork0.2466 ---
obs0.2476 56624 99.66 %-
Displacement parametersBiso mean: 99.23 Å2
Baniso -1Baniso -2Baniso -3
1--32.0258 Å20 Å20 Å2
2---16.6587 Å20 Å2
3---48.6845 Å2
Refine analyzeLuzzati coordinate error obs: 0.676 Å
Refinement stepCycle: 1 / Resolution: 2.7→48.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9109 0 106 0 9215
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.019372HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0512703HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4442SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes216HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1356HARMONIC5
X-RAY DIFFRACTIONt_it9372HARMONIC20
X-RAY DIFFRACTIONt_nbd2SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.46
X-RAY DIFFRACTIONt_other_torsion3.59
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1289SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact11117SEMIHARMONIC4
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3753 226 5.53 %
Rwork0.3527 3861 -
all0.3539 4087 -
obs--99.66 %

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